1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/changeset/66038323cb43/ changeset: 66038323cb43 user: dan date: 2011-11-21 15:50:37 summary: Update modified generic GATK 1.3 arguments. affected #: 13 files

diff -r fd76a44745351d69f8abbccc14fec833e83b469a -r 66038323cb438066cb76e255fd436fc245056bfd tools/gatk/count_covariates.xml --- a/tools/gatk/count_covariates.xml +++ b/tools/gatk/count_covariates.xml @@ -46,9 +46,13 @@

##start standard gatk options #if $gatk_param_type.gatk_param_type_selector == "advanced": - #for $sample_metadata in $gatk_param_type.sample_metadata: - -p '--sample_metadata "${sample_metadata.sample_metadata_file}"' + #for $pedigree in $gatk_param_type.pedigree: + -p '--pedigree "${pedigree.pedigree_file}"' #end for + #for $pedigree_string in $gatk_param_type.pedigree_string_repeat: + -p '--pedigreeString "${pedigree_string.pedigree_string}"' + #end for + -p '--pedigreeValidationType "${gatk_param_type.pedigree_validation_type}"' #for $read_filter in $gatk_param_type.read_filter: -p '--read_filter "${read_filter.read_filter_type.read_filter_type_selector}" ###raise Exception( str( dir( $read_filter ) ) ) @@ -67,7 +71,7 @@ -d "--excludeIntervals" "${input_intervals.input_exclude_intervals}" "${input_intervals.input_exclude_intervals.ext}" "input_exlude_intervals_${interval_count}" #end for

- -p '--BTI_merge_rule "${gatk_param_type.BTI_merge_rule}"' + -p '--interval_set_rule "${gatk_param_type.interval_set_rule}"'

-p '--downsampling_type "${gatk_param_type.downsampling_type.downsampling_type_selector}"' #if str( $gatk_param_type.downsampling_type.downsampling_type_selector ) != "NONE": @@ -213,9 +217,16 @@ <!-- Do nothing here --></when><when value="advanced"> - <repeat name="sample_metadata" title="Sample Metadata"> - <param name="sample_metadata_file" type="data" format="txt" label="Sample file in JSON format" /> + <repeat name="pedigree" title="Pedigree file"> + <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples" /></repeat> + <repeat name="pedigree_string_repeat" title="Pedigree string"> + <param name="pedigree_string" type="text" value="" label="Pedigree string for samples" /> + </repeat> + <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information"> + <option value="STRICT" selected="True">STRICT</option> + <option value="SILENT">SILENT</option> + </param><repeat name="read_filter" title="Read Filter"><conditional name="read_filter_type"><param name="read_filter_type_selector" type="select" label="Read Filter Type"> @@ -237,7 +248,7 @@ <param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" /></repeat>

- <param name="BTI_merge_rule" type="select" label="BTI merge rule"> + <param name="interval_set_rule" type="select" label="Interval set rule"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param>

diff -r fd76a44745351d69f8abbccc14fec833e83b469a -r 66038323cb438066cb76e255fd436fc245056bfd tools/gatk/depth_of_coverage.xml --- a/tools/gatk/depth_of_coverage.xml +++ b/tools/gatk/depth_of_coverage.xml @@ -37,9 +37,13 @@

##start standard gatk options #if $gatk_param_type.gatk_param_type_selector == "advanced": - #for $sample_metadata in $gatk_param_type.sample_metadata: - -p '--sample_metadata "${sample_metadata.sample_metadata_file}"' + #for $pedigree in $gatk_param_type.pedigree: + -p '--pedigree "${pedigree.pedigree_file}"' #end for + #for $pedigree_string in $gatk_param_type.pedigree_string_repeat: + -p '--pedigreeString "${pedigree_string.pedigree_string}"' + #end for + -p '--pedigreeValidationType "${gatk_param_type.pedigree_validation_type}"' #for $read_filter in $gatk_param_type.read_filter: -p '--read_filter "${read_filter.read_filter_type.read_filter_type_selector}" ###raise Exception( str( dir( $read_filter ) ) ) @@ -58,7 +62,7 @@ -d "--excludeIntervals" "${input_intervals.input_exclude_intervals}" "${input_intervals.input_exclude_intervals.ext}" "input_exlude_intervals_${interval_count}" #end for

- -p '--BTI_merge_rule "${gatk_param_type.BTI_merge_rule}"' + -p '--interval_set_rule "${gatk_param_type.interval_set_rule}"'

-p '--downsampling_type "${gatk_param_type.downsampling_type.downsampling_type_selector}"' #if str( $gatk_param_type.downsampling_type.downsampling_type_selector ) != "NONE": @@ -229,9 +233,16 @@ <!-- Do nothing here --></when><when value="advanced"> - <repeat name="sample_metadata" title="Sample Metadata"> - <param name="sample_metadata_file" type="data" format="txt" label="Sample file in JSON format" /> + <repeat name="pedigree" title="Pedigree file"> + <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples" /></repeat> + <repeat name="pedigree_string_repeat" title="Pedigree string"> + <param name="pedigree_string" type="text" value="" label="Pedigree string for samples" /> + </repeat> + <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information"> + <option value="STRICT" selected="True">STRICT</option> + <option value="SILENT">SILENT</option> + </param><repeat name="read_filter" title="Read Filter"><conditional name="read_filter_type"><param name="read_filter_type_selector" type="select" label="Read Filter Type"> @@ -253,7 +264,7 @@ <param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" /></repeat>

- <param name="BTI_merge_rule" type="select" label="BTI merge rule"> + <param name="interval_set_rule" type="select" label="Interval set rule"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param>

diff -r fd76a44745351d69f8abbccc14fec833e83b469a -r 66038323cb438066cb76e255fd436fc245056bfd tools/gatk/indel_realigner.xml --- a/tools/gatk/indel_realigner.xml +++ b/tools/gatk/indel_realigner.xml @@ -38,9 +38,13 @@

##start standard gatk options #if $gatk_param_type.gatk_param_type_selector == "advanced": - #for $sample_metadata in $gatk_param_type.sample_metadata: - -p '--sample_metadata "${sample_metadata.sample_metadata_file}"' + #for $pedigree in $gatk_param_type.pedigree: + -p '--pedigree "${pedigree.pedigree_file}"' #end for + #for $pedigree_string in $gatk_param_type.pedigree_string_repeat: + -p '--pedigreeString "${pedigree_string.pedigree_string}"' + #end for + -p '--pedigreeValidationType "${gatk_param_type.pedigree_validation_type}"' #for $read_filter in $gatk_param_type.read_filter: -p '--read_filter "${read_filter.read_filter_type.read_filter_type_selector}" ###raise Exception( str( dir( $read_filter ) ) ) @@ -59,7 +63,7 @@ -d "--excludeIntervals" "${input_intervals.input_exclude_intervals}" "${input_intervals.input_exclude_intervals.ext}" "input_exlude_intervals_${interval_count}" #end for

- -p '--BTI_merge_rule "${gatk_param_type.BTI_merge_rule}"' + -p '--interval_set_rule "${gatk_param_type.interval_set_rule}"'

-p '--downsampling_type "${gatk_param_type.downsampling_type.downsampling_type_selector}"' #if str( $gatk_param_type.downsampling_type.downsampling_type_selector ) != "NONE": @@ -176,9 +180,16 @@ <!-- Do nothing here --></when><when value="advanced"> - <repeat name="sample_metadata" title="Sample Metadata"> - <param name="sample_metadata_file" type="data" format="txt" label="Sample file in JSON format" /> + <repeat name="pedigree" title="Pedigree file"> + <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples" /></repeat> + <repeat name="pedigree_string_repeat" title="Pedigree string"> + <param name="pedigree_string" type="text" value="" label="Pedigree string for samples" /> + </repeat> + <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information"> + <option value="STRICT" selected="True">STRICT</option> + <option value="SILENT">SILENT</option> + </param><repeat name="read_filter" title="Read Filter"><conditional name="read_filter_type"><param name="read_filter_type_selector" type="select" label="Read Filter Type"> @@ -200,7 +211,7 @@ <param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" /></repeat>

- <param name="BTI_merge_rule" type="select" label="BTI merge rule"> + <param name="interval_set_rule" type="select" label="Interval set rule"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param>

diff -r fd76a44745351d69f8abbccc14fec833e83b469a -r 66038323cb438066cb76e255fd436fc245056bfd tools/gatk/realigner_target_creator.xml --- a/tools/gatk/realigner_target_creator.xml +++ b/tools/gatk/realigner_target_creator.xml @@ -35,9 +35,13 @@

##start standard gatk options #if $gatk_param_type.gatk_param_type_selector == "advanced": - #for $sample_metadata in $gatk_param_type.sample_metadata: - -p '--sample_metadata "${sample_metadata.sample_metadata_file}"' + #for $pedigree in $gatk_param_type.pedigree: + -p '--pedigree "${pedigree.pedigree_file}"' #end for + #for $pedigree_string in $gatk_param_type.pedigree_string_repeat: + -p '--pedigreeString "${pedigree_string.pedigree_string}"' + #end for + -p '--pedigreeValidationType "${gatk_param_type.pedigree_validation_type}"' #for $read_filter in $gatk_param_type.read_filter: -p '--read_filter "${read_filter.read_filter_type.read_filter_type_selector}" ###raise Exception( str( dir( $read_filter ) ) ) @@ -56,7 +60,7 @@ -d "--excludeIntervals" "${input_intervals.input_exclude_intervals}" "${input_intervals.input_exclude_intervals.ext}" "input_exlude_intervals_${interval_count}" #end for

- -p '--BTI_merge_rule "${gatk_param_type.BTI_merge_rule}"' + -p '--interval_set_rule "${gatk_param_type.interval_set_rule}"'

-p '--downsampling_type "${gatk_param_type.downsampling_type.downsampling_type_selector}"' #if str( $gatk_param_type.downsampling_type.downsampling_type_selector ) != "NONE": @@ -162,9 +166,16 @@ <!-- Do nothing here --></when><when value="advanced"> - <repeat name="sample_metadata" title="Sample Metadata"> - <param name="sample_metadata_file" type="data" format="txt" label="Sample file in JSON format" /> + <repeat name="pedigree" title="Pedigree file"> + <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples" /></repeat> + <repeat name="pedigree_string_repeat" title="Pedigree string"> + <param name="pedigree_string" type="text" value="" label="Pedigree string for samples" /> + </repeat> + <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information"> + <option value="STRICT" selected="True">STRICT</option> + <option value="SILENT">SILENT</option> + </param><repeat name="read_filter" title="Read Filter"><conditional name="read_filter_type"><param name="read_filter_type_selector" type="select" label="Read Filter Type"> @@ -186,7 +197,7 @@ <param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" /></repeat>

- <param name="BTI_merge_rule" type="select" label="BTI merge rule"> + <param name="interval_set_rule" type="select" label="Interval set rule"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param>

diff -r fd76a44745351d69f8abbccc14fec833e83b469a -r 66038323cb438066cb76e255fd436fc245056bfd tools/gatk/table_recalibration.xml --- a/tools/gatk/table_recalibration.xml +++ b/tools/gatk/table_recalibration.xml @@ -23,9 +23,13 @@ ' ##start standard gatk options #if $gatk_param_type.gatk_param_type_selector == "advanced": - #for $sample_metadata in $gatk_param_type.sample_metadata: - -p '--sample_metadata "${sample_metadata.sample_metadata_file}"' + #for $pedigree in $gatk_param_type.pedigree: + -p '--pedigree "${pedigree.pedigree_file}"' #end for + #for $pedigree_string in $gatk_param_type.pedigree_string_repeat: + -p '--pedigreeString "${pedigree_string.pedigree_string}"' + #end for + -p '--pedigreeValidationType "${gatk_param_type.pedigree_validation_type}"' #for $read_filter in $gatk_param_type.read_filter: -p '--read_filter "${read_filter.read_filter_type.read_filter_type_selector}" ###raise Exception( str( dir( $read_filter ) ) ) @@ -44,7 +48,7 @@ -d "--excludeIntervals" "${input_intervals.input_exclude_intervals}" "${input_intervals.input_exclude_intervals.ext}" "input_exlude_intervals_${interval_count}" #end for

- -p '--BTI_merge_rule "${gatk_param_type.BTI_merge_rule}"' + -p '--interval_set_rule "${gatk_param_type.interval_set_rule}"'

-p '--downsampling_type "${gatk_param_type.downsampling_type.downsampling_type_selector}"' #if str( $gatk_param_type.downsampling_type.downsampling_type_selector ) != "NONE": @@ -144,9 +148,16 @@ <!-- Do nothing here --></when><when value="advanced"> - <repeat name="sample_metadata" title="Sample Metadata"> - <param name="sample_metadata_file" type="data" format="txt" label="Sample file in JSON format" /> + <repeat name="pedigree" title="Pedigree file"> + <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples" /></repeat> + <repeat name="pedigree_string_repeat" title="Pedigree string"> + <param name="pedigree_string" type="text" value="" label="Pedigree string for samples" /> + </repeat> + <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information"> + <option value="STRICT" selected="True">STRICT</option> + <option value="SILENT">SILENT</option> + </param><repeat name="read_filter" title="Read Filter"><conditional name="read_filter_type"><param name="read_filter_type_selector" type="select" label="Read Filter Type"> @@ -168,7 +179,7 @@ <param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" /></repeat>

- <param name="BTI_merge_rule" type="select" label="BTI merge rule"> + <param name="interval_set_rule" type="select" label="Interval set rule"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param>

diff -r fd76a44745351d69f8abbccc14fec833e83b469a -r 66038323cb438066cb76e255fd436fc245056bfd tools/gatk/unified_genotyper.xml --- a/tools/gatk/unified_genotyper.xml +++ b/tools/gatk/unified_genotyper.xml @@ -41,9 +41,13 @@

##start standard gatk options #if $gatk_param_type.gatk_param_type_selector == "advanced": - #for $sample_metadata in $gatk_param_type.sample_metadata: - -p '--sample_metadata "${sample_metadata.sample_metadata_file}"' + #for $pedigree in $gatk_param_type.pedigree: + -p '--pedigree "${pedigree.pedigree_file}"' #end for + #for $pedigree_string in $gatk_param_type.pedigree_string_repeat: + -p '--pedigreeString "${pedigree_string.pedigree_string}"' + #end for + -p '--pedigreeValidationType "${gatk_param_type.pedigree_validation_type}"' #for $read_filter in $gatk_param_type.read_filter: -p '--read_filter "${read_filter.read_filter_type.read_filter_type_selector}" ###raise Exception( str( dir( $read_filter ) ) ) @@ -62,7 +66,7 @@ -d "--excludeIntervals" "${input_intervals.input_exclude_intervals}" "${input_intervals.input_exclude_intervals.ext}" "input_exlude_intervals_${interval_count}" #end for

- -p '--BTI_merge_rule "${gatk_param_type.BTI_merge_rule}"' + -p '--interval_set_rule "${gatk_param_type.interval_set_rule}"'

-p '--downsampling_type "${gatk_param_type.downsampling_type.downsampling_type_selector}"' #if str( $gatk_param_type.downsampling_type.downsampling_type_selector ) != "NONE": @@ -201,9 +205,16 @@ <!-- Do nothing here --></when><when value="advanced"> - <repeat name="sample_metadata" title="Sample Metadata"> - <param name="sample_metadata_file" type="data" format="txt" label="Sample file in JSON format" /> + <repeat name="pedigree" title="Pedigree file"> + <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples" /></repeat> + <repeat name="pedigree_string_repeat" title="Pedigree string"> + <param name="pedigree_string" type="text" value="" label="Pedigree string for samples" /> + </repeat> + <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information"> + <option value="STRICT" selected="True">STRICT</option> + <option value="SILENT">SILENT</option> + </param><repeat name="read_filter" title="Read Filter"><conditional name="read_filter_type"><param name="read_filter_type_selector" type="select" label="Read Filter Type"> @@ -225,7 +236,7 @@ <param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" /></repeat>

- <param name="BTI_merge_rule" type="select" label="BTI merge rule"> + <param name="interval_set_rule" type="select" label="Interval set rule"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param>

diff -r fd76a44745351d69f8abbccc14fec833e83b469a -r 66038323cb438066cb76e255fd436fc245056bfd tools/gatk/variant_annotator.xml --- a/tools/gatk/variant_annotator.xml +++ b/tools/gatk/variant_annotator.xml @@ -76,9 +76,13 @@

##start standard gatk options #if $gatk_param_type.gatk_param_type_selector == "advanced": - #for $sample_metadata in $gatk_param_type.sample_metadata: - -p '--sample_metadata "${sample_metadata.sample_metadata_file}"' + #for $pedigree in $gatk_param_type.pedigree: + -p '--pedigree "${pedigree.pedigree_file}"' #end for + #for $pedigree_string in $gatk_param_type.pedigree_string_repeat: + -p '--pedigreeString "${pedigree_string.pedigree_string}"' + #end for + -p '--pedigreeValidationType "${gatk_param_type.pedigree_validation_type}"' #for $read_filter in $gatk_param_type.read_filter: -p '--read_filter "${read_filter.read_filter_type.read_filter_type_selector}" ###raise Exception( str( dir( $read_filter ) ) ) @@ -97,7 +101,7 @@ -d "--excludeIntervals" "${input_intervals.input_exclude_intervals}" "${input_intervals.input_exclude_intervals.ext}" "input_exlude_intervals_${interval_count}" #end for

- -p '--BTI_merge_rule "${gatk_param_type.BTI_merge_rule}"' + -p '--interval_set_rule "${gatk_param_type.interval_set_rule}"'

-p '--downsampling_type "${gatk_param_type.downsampling_type.downsampling_type_selector}"' #if str( $gatk_param_type.downsampling_type.downsampling_type_selector ) != "NONE": @@ -262,9 +266,16 @@ <!-- Do nothing here --></when><when value="advanced"> - <repeat name="sample_metadata" title="Sample Metadata"> - <param name="sample_metadata_file" type="data" format="txt" label="Sample file in JSON format" /> + <repeat name="pedigree" title="Pedigree file"> + <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples" /></repeat> + <repeat name="pedigree_string_repeat" title="Pedigree string"> + <param name="pedigree_string" type="text" value="" label="Pedigree string for samples" /> + </repeat> + <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information"> + <option value="STRICT" selected="True">STRICT</option> + <option value="SILENT">SILENT</option> + </param><repeat name="read_filter" title="Read Filter"><conditional name="read_filter_type"><param name="read_filter_type_selector" type="select" label="Read Filter Type"> @@ -286,7 +297,7 @@ <param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" /></repeat>

- <param name="BTI_merge_rule" type="select" label="BTI merge rule"> + <param name="interval_set_rule" type="select" label="Interval set rule"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param>

diff -r fd76a44745351d69f8abbccc14fec833e83b469a -r 66038323cb438066cb76e255fd436fc245056bfd tools/gatk/variant_apply_recalibration.xml --- a/tools/gatk/variant_apply_recalibration.xml +++ b/tools/gatk/variant_apply_recalibration.xml @@ -24,9 +24,13 @@

##start standard gatk options #if $gatk_param_type.gatk_param_type_selector == "advanced": - #for $sample_metadata in $gatk_param_type.sample_metadata: - -p '--sample_metadata "${sample_metadata.sample_metadata_file}"' + #for $pedigree in $gatk_param_type.pedigree: + -p '--pedigree "${pedigree.pedigree_file}"' #end for + #for $pedigree_string in $gatk_param_type.pedigree_string_repeat: + -p '--pedigreeString "${pedigree_string.pedigree_string}"' + #end for + -p '--pedigreeValidationType "${gatk_param_type.pedigree_validation_type}"' #for $read_filter in $gatk_param_type.read_filter: -p '--read_filter "${read_filter.read_filter_type.read_filter_type_selector}" ###raise Exception( str( dir( $read_filter ) ) ) @@ -45,7 +49,7 @@ -d "--excludeIntervals" "${input_intervals.input_exclude_intervals}" "${input_intervals.input_exclude_intervals.ext}" "input_exlude_intervals_${interval_count}" #end for

- -p '--BTI_merge_rule "${gatk_param_type.BTI_merge_rule}"' + -p '--interval_set_rule "${gatk_param_type.interval_set_rule}"'

-p '--downsampling_type "${gatk_param_type.downsampling_type.downsampling_type_selector}"' #if str( $gatk_param_type.downsampling_type.downsampling_type_selector ) != "NONE": @@ -126,9 +130,16 @@ <!-- Do nothing here --></when><when value="advanced"> - <repeat name="sample_metadata" title="Sample Metadata"> - <param name="sample_metadata_file" type="data" format="txt" label="Sample file in JSON format" /> + <repeat name="pedigree" title="Pedigree file"> + <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples" /></repeat> + <repeat name="pedigree_string_repeat" title="Pedigree string"> + <param name="pedigree_string" type="text" value="" label="Pedigree string for samples" /> + </repeat> + <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information"> + <option value="STRICT" selected="True">STRICT</option> + <option value="SILENT">SILENT</option> + </param><repeat name="read_filter" title="Read Filter"><conditional name="read_filter_type"><param name="read_filter_type_selector" type="select" label="Read Filter Type"> @@ -150,7 +161,7 @@ <param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" /></repeat>

- <param name="BTI_merge_rule" type="select" label="BTI merge rule"> + <param name="interval_set_rule" type="select" label="Interval set rule"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param>

diff -r fd76a44745351d69f8abbccc14fec833e83b469a -r 66038323cb438066cb76e255fd436fc245056bfd tools/gatk/variant_combine.xml --- a/tools/gatk/variant_combine.xml +++ b/tools/gatk/variant_combine.xml @@ -30,9 +30,13 @@

##start standard gatk options #if $gatk_param_type.gatk_param_type_selector == "advanced": - #for $sample_metadata in $gatk_param_type.sample_metadata: - -p '--sample_metadata "${sample_metadata.sample_metadata_file}"' + #for $pedigree in $gatk_param_type.pedigree: + -p '--pedigree "${pedigree.pedigree_file}"' #end for + #for $pedigree_string in $gatk_param_type.pedigree_string_repeat: + -p '--pedigreeString "${pedigree_string.pedigree_string}"' + #end for + -p '--pedigreeValidationType "${gatk_param_type.pedigree_validation_type}"' #for $read_filter in $gatk_param_type.read_filter: -p '--read_filter "${read_filter.read_filter_type.read_filter_type_selector}" ###raise Exception( str( dir( $read_filter ) ) ) @@ -51,7 +55,7 @@ -d "--excludeIntervals" "${input_intervals.input_exclude_intervals}" "${input_intervals.input_exclude_intervals.ext}" "input_exlude_intervals_${interval_count}" #end for

- -p '--BTI_merge_rule "${gatk_param_type.BTI_merge_rule}"' + -p '--interval_set_rule "${gatk_param_type.interval_set_rule}"'

-p '--downsampling_type "${gatk_param_type.downsampling_type.downsampling_type_selector}"' #if str( $gatk_param_type.downsampling_type.downsampling_type_selector ) != "NONE": @@ -146,9 +150,16 @@ <!-- Do nothing here --></when><when value="advanced"> - <repeat name="sample_metadata" title="Sample Metadata"> - <param name="sample_metadata_file" type="data" format="txt" label="Sample file in JSON format" /> + <repeat name="pedigree" title="Pedigree file"> + <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples" /></repeat> + <repeat name="pedigree_string_repeat" title="Pedigree string"> + <param name="pedigree_string" type="text" value="" label="Pedigree string for samples" /> + </repeat> + <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information"> + <option value="STRICT" selected="True">STRICT</option> + <option value="SILENT">SILENT</option> + </param><repeat name="read_filter" title="Read Filter"><conditional name="read_filter_type"><param name="read_filter_type_selector" type="select" label="Read Filter Type"> @@ -170,7 +181,7 @@ <param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" /></repeat>

- <param name="BTI_merge_rule" type="select" label="BTI merge rule"> + <param name="interval_set_rule" type="select" label="Interval set rule"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param>

diff -r fd76a44745351d69f8abbccc14fec833e83b469a -r 66038323cb438066cb76e255fd436fc245056bfd tools/gatk/variant_eval.xml --- a/tools/gatk/variant_eval.xml +++ b/tools/gatk/variant_eval.xml @@ -43,9 +43,13 @@

##start standard gatk options #if $gatk_param_type.gatk_param_type_selector == "advanced": - #for $sample_metadata in $gatk_param_type.sample_metadata: - -p '--sample_metadata "${sample_metadata.sample_metadata_file}"' + #for $pedigree in $gatk_param_type.pedigree: + -p '--pedigree "${pedigree.pedigree_file}"' #end for + #for $pedigree_string in $gatk_param_type.pedigree_string_repeat: + -p '--pedigreeString "${pedigree_string.pedigree_string}"' + #end for + -p '--pedigreeValidationType "${gatk_param_type.pedigree_validation_type}"' #for $read_filter in $gatk_param_type.read_filter: -p '--read_filter "${read_filter.read_filter_type.read_filter_type_selector}" ###raise Exception( str( dir( $read_filter ) ) ) @@ -64,7 +68,7 @@ -d "--excludeIntervals" "${input_intervals.input_exclude_intervals}" "${input_intervals.input_exclude_intervals.ext}" "input_exlude_intervals_${interval_count}" #end for

- -p '--BTI_merge_rule "${gatk_param_type.BTI_merge_rule}"' + -p '--interval_set_rule "${gatk_param_type.interval_set_rule}"'

-p '--downsampling_type "${gatk_param_type.downsampling_type.downsampling_type_selector}"' #if str( $gatk_param_type.downsampling_type.downsampling_type_selector ) != "NONE": @@ -204,9 +208,16 @@ <!-- Do nothing here --></when><when value="advanced"> - <repeat name="sample_metadata" title="Sample Metadata"> - <param name="sample_metadata_file" type="data" format="txt" label="Sample file in JSON format" /> + <repeat name="pedigree" title="Pedigree file"> + <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples" /></repeat> + <repeat name="pedigree_string_repeat" title="Pedigree string"> + <param name="pedigree_string" type="text" value="" label="Pedigree string for samples" /> + </repeat> + <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information"> + <option value="STRICT" selected="True">STRICT</option> + <option value="SILENT">SILENT</option> + </param><repeat name="read_filter" title="Read Filter"><conditional name="read_filter_type"><param name="read_filter_type_selector" type="select" label="Read Filter Type"> @@ -228,7 +239,7 @@ <param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" /></repeat>

- <param name="BTI_merge_rule" type="select" label="BTI merge rule"> + <param name="interval_set_rule" type="select" label="Interval set rule"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param>

diff -r fd76a44745351d69f8abbccc14fec833e83b469a -r 66038323cb438066cb76e255fd436fc245056bfd tools/gatk/variant_filtration.xml --- a/tools/gatk/variant_filtration.xml +++ b/tools/gatk/variant_filtration.xml @@ -37,9 +37,13 @@

##start standard gatk options #if $gatk_param_type.gatk_param_type_selector == "advanced": - #for $sample_metadata in $gatk_param_type.sample_metadata: - -p '--sample_metadata "${sample_metadata.sample_metadata_file}"' + #for $pedigree in $gatk_param_type.pedigree: + -p '--pedigree "${pedigree.pedigree_file}"' #end for + #for $pedigree_string in $gatk_param_type.pedigree_string_repeat: + -p '--pedigreeString "${pedigree_string.pedigree_string}"' + #end for + -p '--pedigreeValidationType "${gatk_param_type.pedigree_validation_type}"' #for $read_filter in $gatk_param_type.read_filter: -p '--read_filter "${read_filter.read_filter_type.read_filter_type_selector}" ###raise Exception( str( dir( $read_filter ) ) ) @@ -58,7 +62,7 @@ -d "--excludeIntervals" "${input_intervals.input_exclude_intervals}" "${input_intervals.input_exclude_intervals.ext}" "input_exlude_intervals_${interval_count}" #end for

- -p '--BTI_merge_rule "${gatk_param_type.BTI_merge_rule}"' + -p '--interval_set_rule "${gatk_param_type.interval_set_rule}"'

-p '--downsampling_type "${gatk_param_type.downsampling_type.downsampling_type_selector}"' #if str( $gatk_param_type.downsampling_type.downsampling_type_selector ) != "NONE": @@ -160,9 +164,16 @@ <!-- Do nothing here --></when><when value="advanced"> - <repeat name="sample_metadata" title="Sample Metadata"> - <param name="sample_metadata_file" type="data" format="txt" label="Sample file in JSON format" /> + <repeat name="pedigree" title="Pedigree file"> + <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples" /></repeat> + <repeat name="pedigree_string_repeat" title="Pedigree string"> + <param name="pedigree_string" type="text" value="" label="Pedigree string for samples" /> + </repeat> + <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information"> + <option value="STRICT" selected="True">STRICT</option> + <option value="SILENT">SILENT</option> + </param><repeat name="read_filter" title="Read Filter"><conditional name="read_filter_type"><param name="read_filter_type_selector" type="select" label="Read Filter Type"> @@ -184,7 +195,7 @@ <param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" /></repeat>

- <param name="BTI_merge_rule" type="select" label="BTI merge rule"> + <param name="interval_set_rule" type="select" label="Interval set rule"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param>

diff -r fd76a44745351d69f8abbccc14fec833e83b469a -r 66038323cb438066cb76e255fd436fc245056bfd tools/gatk/variant_recalibrator.xml --- a/tools/gatk/variant_recalibrator.xml +++ b/tools/gatk/variant_recalibrator.xml @@ -45,9 +45,13 @@

##start standard gatk options #if $gatk_param_type.gatk_param_type_selector == "advanced": - #for $sample_metadata in $gatk_param_type.sample_metadata: - -p '--sample_metadata "${sample_metadata.sample_metadata_file}"' + #for $pedigree in $gatk_param_type.pedigree: + -p '--pedigree "${pedigree.pedigree_file}"' #end for + #for $pedigree_string in $gatk_param_type.pedigree_string_repeat: + -p '--pedigreeString "${pedigree_string.pedigree_string}"' + #end for + -p '--pedigreeValidationType "${gatk_param_type.pedigree_validation_type}"' #for $read_filter in $gatk_param_type.read_filter: -p '--read_filter "${read_filter.read_filter_type.read_filter_type_selector}" ###raise Exception( str( dir( $read_filter ) ) ) @@ -66,7 +70,7 @@ -d "--excludeIntervals" "${input_intervals.input_exclude_intervals}" "${input_intervals.input_exclude_intervals.ext}" "input_exlude_intervals_${interval_count}" #end for

- -p '--BTI_merge_rule "${gatk_param_type.BTI_merge_rule}"' + -p '--interval_set_rule "${gatk_param_type.interval_set_rule}"'

-p '--downsampling_type "${gatk_param_type.downsampling_type.downsampling_type_selector}"' #if str( $gatk_param_type.downsampling_type.downsampling_type_selector ) != "NONE": @@ -390,9 +394,16 @@ <!-- Do nothing here --></when><when value="advanced"> - <repeat name="sample_metadata" title="Sample Metadata"> - <param name="sample_metadata_file" type="data" format="txt" label="Sample file in JSON format" /> + <repeat name="pedigree" title="Pedigree file"> + <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples" /></repeat> + <repeat name="pedigree_string_repeat" title="Pedigree string"> + <param name="pedigree_string" type="text" value="" label="Pedigree string for samples" /> + </repeat> + <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information"> + <option value="STRICT" selected="True">STRICT</option> + <option value="SILENT">SILENT</option> + </param><repeat name="read_filter" title="Read Filter"><conditional name="read_filter_type"><param name="read_filter_type_selector" type="select" label="Read Filter Type"> @@ -414,7 +425,7 @@ <param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" /></repeat>

- <param name="BTI_merge_rule" type="select" label="BTI merge rule"> + <param name="interval_set_rule" type="select" label="Interval set rule"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param>

diff -r fd76a44745351d69f8abbccc14fec833e83b469a -r 66038323cb438066cb76e255fd436fc245056bfd tools/gatk/variants_validate.xml --- a/tools/gatk/variants_validate.xml +++ b/tools/gatk/variants_validate.xml @@ -30,9 +30,13 @@

##start standard gatk options #if $gatk_param_type.gatk_param_type_selector == "advanced": - #for $sample_metadata in $gatk_param_type.sample_metadata: - -p '--sample_metadata "${sample_metadata.sample_metadata_file}"' + #for $pedigree in $gatk_param_type.pedigree: + -p '--pedigree "${pedigree.pedigree_file}"' #end for + #for $pedigree_string in $gatk_param_type.pedigree_string_repeat: + -p '--pedigreeString "${pedigree_string.pedigree_string}"' + #end for + -p '--pedigreeValidationType "${gatk_param_type.pedigree_validation_type}"' #for $read_filter in $gatk_param_type.read_filter: -p '--read_filter "${read_filter.read_filter_type.read_filter_type_selector}" ###raise Exception( str( dir( $read_filter ) ) ) @@ -51,7 +55,7 @@ -d "--excludeIntervals" "${input_intervals.input_exclude_intervals}" "${input_intervals.input_exclude_intervals.ext}" "input_exlude_intervals_${interval_count}" #end for

- -p '--BTI_merge_rule "${gatk_param_type.BTI_merge_rule}"' + -p '--interval_set_rule "${gatk_param_type.interval_set_rule}"'

-p '--downsampling_type "${gatk_param_type.downsampling_type.downsampling_type_selector}"' #if str( $gatk_param_type.downsampling_type.downsampling_type_selector ) != "NONE": @@ -130,9 +134,16 @@ <!-- Do nothing here --></when><when value="advanced"> - <repeat name="sample_metadata" title="Sample Metadata"> - <param name="sample_metadata_file" type="data" format="txt" label="Sample file in JSON format" /> + <repeat name="pedigree" title="Pedigree file"> + <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples" /></repeat> + <repeat name="pedigree_string_repeat" title="Pedigree string"> + <param name="pedigree_string" type="text" value="" label="Pedigree string for samples" /> + </repeat> + <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information"> + <option value="STRICT" selected="True">STRICT</option> + <option value="SILENT">SILENT</option> + </param><repeat name="read_filter" title="Read Filter"><conditional name="read_filter_type"><param name="read_filter_type_selector" type="select" label="Read Filter Type"> @@ -154,7 +165,7 @@ <param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" /></repeat>

- <param name="BTI_merge_rule" type="select" label="BTI merge rule"> + <param name="interval_set_rule" type="select" label="Interval set rule"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param>

Repository URL: https://bitbucket.org/galaxy/galaxy-central/

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